In Newfoundland and Labrador, allegations of political interference in the hiring of a new president cast doubt on Memorial University's independence from the government.
In British Columbia, the provincial government circulates a letter of expectations to universities hoping to qualify for additional education funding.
In Saskatchewan, concerns are raised about the influence the Federation of Saskatchewan First Nations has on the First Nations University in Regina.
Those are just a few of the examples of what some academics believe to be an assault on the historic autonomy of universities, a tradition that usually elevates universities above political decisions.
"Sometimes autonomy is confused with accountability," says David Robinson, assistant executive director of the Canadian Association of University Teachers.
The latest example to raise the eyebrows of those concerned with academic freedom is at Memorial University in St. John's, N.L., where there have been calls for the chairman of the board of regents and Education Minister Joan Burke to step down after Burke interviewed and rejected two candidates for the job of president.
Robinson said the CAUT has written to Burke asking to meet with her and Premier Danny Williams about their concerns over university autonomy.
But he said what sets this incident apart from other forms of political interference in the operation of universities is that it's out in the open. Other forms are more subtle, yet just as hazardous to the tradition of academic freedom.
"But it's not difficult to imagine that a government could impose performance indicators on a university when it goes to government for funding," he said.
In May, the British Columbia government sent what it called a Government Letter of Expectations to universities in that province setting out specifically how universities should fulfil government priorities.
The letters replaced the traditional annual budget letter that outlined what the operating grant would be, how many students each institution was expected to serve and the annual capital allowance.
The letter was widely criticized, especially by the Confederation of University Faculty Associations of British Columbia, which it a dangerous and unprecedented intrusion into the governance of public universities.
In Saskatchewan, meanwhile, the First Nations University has had its probation status lifted after a year of working toward a better governance structure independent from the Federation of Saskatchewan First Nations.
The Association of Universities and Colleges of Canada placed the Regina-based institution on probation over concerns the First Nations advocacy group was exerting undue influence on the university's governance, which influenced its institutional autonomy and academic freedom.
The matter was resolved when Lyle Whitefish resigned from the board of the university. Whitefish also served as the vice-chief of education for the federation, which the AUCC called a clear violation of the university's autonomy.
And while the NDP in Newfoundland has called for the resignation of the chairman of Memorial's board of regents, faculty association president Ross Klein says that is less important than assurances from the government it will allow the search process to carry on without interference.
"It is time for the government to make a very bold statement and apologize for what it's done," Klein said, adding he's received support from other faculty associations and university faculties urging Memorial University's association to continue fighting.
The controversy could also damage Memorial's search for a new president.
"Who wants to be the CEO of a major organization with the government telling them what they can or can't do?" Klein said.